Merge branch 'master' into sqlite
This commit is contained in:
Joey Hess
commit
6147130e86
26 changed files with 355 additions and 37 deletions
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@ -0,0 +1,43 @@
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[[!comment format=mdwn
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username="yarikoptic"
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avatar="http://cdn.libravatar.org/avatar/f11e9c84cb18d26a1748c33b48c924b4"
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subject="the issue persists"
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date="2019-11-01T18:12:27Z"
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content="""
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Ran into the same problem again, and it is not clear to me either connection caching is enabled or not (and why?):
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[[!format sh \"\"\"
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[d31548v@discovery7 bids]$ git -c annex.sshcaching=true annex --debug get -J2 --from=origin sub-sid000005
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[2019-11-01 14:10:56.178577] read: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"show-ref\",\"git-annex\"]
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[2019-11-01 14:10:56.475956] process done ExitSuccess
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[2019-11-01 14:10:56.47622] read: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"show-ref\",\"--hash\",\"refs/heads/git-annex\"]
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[2019-11-01 14:10:56.836271] process done ExitSuccess
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[2019-11-01 14:10:56.865928] read: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"log\",\"refs/heads/git-annex..8a694d5c54eb81b1e5c5446fa63bdcd13daa34b3\",\"--pretty=%H\",\"-n1\"]
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[2019-11-01 14:10:57.229787] process done ExitSuccess
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[2019-11-01 14:10:57.234655] chat: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"cat-file\",\"--batch\"]
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[2019-11-01 14:10:57.23592] chat: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"cat-file\",\"--batch-check=%(objectname) %(objecttype) %(objectsize)\"]
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[2019-11-01 14:10:57.546203] read: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"symbolic-ref\",\"-q\",\"HEAD\"]
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[2019-11-01 14:10:57.780246] process done ExitSuccess
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[2019-11-01 14:10:57.780454] read: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"show-ref\",\"refs/heads/master\"]
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[2019-11-01 14:10:58.097345] process done ExitSuccess
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[2019-11-01 14:10:58.09754] read: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"ls-files\",\"--cached\",\"-z\",\"--\",\"sub-sid000005\"]
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[2019-11-01 14:10:58.298181] chat: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"cat-file\",\"--batch\"]
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[2019-11-01 14:10:58.29998] chat: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"cat-file\",\"--batch-check=%(objectname) %(objecttype) %(objectsize)\"]
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[2019-11-01 14:10:58.305022] chat: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"cat-file\",\"--batch\"]
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[2019-11-01 14:10:58.306024] chat: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"cat-file\",\"--batch-check=%(objectname) %(objecttype) %(objectsize)\"]
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[2019-11-01 14:10:58.62005] chat: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"cat-file\",\"--batch\"]
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[2019-11-01 14:10:58.621714] chat: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"cat-file\",\"--batch-check=%(objectname) %(objecttype) %(objectsize)\"]
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[2019-11-01 14:10:58.632596] chat: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"cat-file\",\"--batch\"]
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[2019-11-01 14:10:58.6338] chat: git [\"--git-dir=.git\",\"--work-tree=.\",\"--literal-pathspecs\",\"cat-file\",\"--batch-check=%(objectname) %(objecttype) %(objectsize)\"]
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get sub-sid000005/ses-actions1/fmap/sub-sid000005_ses-actions1_acq-25mm_magnitude2.nii.gz get sub-sid000005/ses-actions1/fmap/sub-sid000005_ses-actions1_acq-25mm_magnitude1.nii.gz (from origin...) (from origin...)
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[2019-11-01 14:10:59.489719] chat: ssh [\"yohtest@rolando.cns.dartmouth.edu\",\"-T\",\"git-annex-shell 'p2pstdio' '/inbox/BIDS/Haxby/Sam/1021_actions' '--debug' 'fd3f7af9-cf7d-4d7e-8efd-30e6bedf838d' --uuid d839134c-3afe-4456-920a-e280ce0fdf2a\"]
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[2019-11-01 14:10:59.553029] chat: ssh [\"yohtest@rolando.cns.dartmouth.edu\",\"-T\",\"git-annex-shell 'p2pstdio' '/inbox/BIDS/Haxby/Sam/1021_actions' '--debug' 'fd3f7af9-cf7d-4d7e-8efd-30e6bedf838d' --uuid d839134c-3afe-4456-920a-e280ce0fdf2a\"]
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yohtest@rolando.cns.dartmouth.edu's password: yohtest@rolando.cns.dartmouth.edu's password:
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[d31548v@discovery7 bids]$ git annex version
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git-annex version: 7.20191024-g6dc2272
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\"\"\"]]
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Could you hint me on what/where to dig?
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"""]]
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41
doc/bugs/Make_webapp_port_configurable..pl
Normal file
41
doc/bugs/Make_webapp_port_configurable..pl
Normal file
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### Please describe the problem.
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This is more of a feature request then a bug.
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It would be nice and more intuitive if the webapp --listen parameter accepted a port specifier too allowing configuration of the port.
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For my workflow, I thought I would contain all of git annexes dependencies inside a docker image since I'm quite comfortable with docker(and emerge on gentoo took a long time and finally failed). With an unconfigurable dynamic port though, it makes running the webapp subcommand in docker not really viable since I don't want to use docker run's port range mapping feature which will lock all those ports.
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### What steps will reproduce the problem?
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Dockerfile:
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ARG DEBIAN_TAG=buster-slim
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FROM debian:${DEBIAN_TAG}
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RUN set -ex \
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&& apt-get update \
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&& apt-get install -y \
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git \
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git-annex
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docker build -t git-annex:test .
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docker run --rm -it git-annex:test git annex webapp --listen 0.0.0.0:8888
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### What version of git-annex are you using? On what operating system?
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git-annex version: 7.20190129
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build flags: Assistant Webapp Pairing S3(multipartupload)(storageclasses) WebDAV Inotify DBus DesktopNotify TorrentParser MagicMime Feeds Testsuite
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dependency versions: aws-0.20 bloomfilter-2.0.1.0 cryptonite-0.25 DAV-1.3.3 feed-1.0.0.0 ghc-8.4.4 http-client-0.5.13.1 persistent-sqlite-2.8.2 torrent-10000.1.1 uuid-1.3.13 yesod-1.6.0
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### Please provide any additional information below.
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[[!format sh """
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# If you can, paste a complete transcript of the problem occurring here.
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# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log
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# End of transcript or log.
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"""]]
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### Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil' positive end note does wonders)
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git annex seems awesome with the little bit of testing I've done. It seems like the perfect tool for what I want to accomplish. Thanks!
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41
doc/bugs/Make_webapp_port_configurable..sh
Normal file
41
doc/bugs/Make_webapp_port_configurable..sh
Normal file
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### Please describe the problem.
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This is more of a feature request then a bug.
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It would be nice and more intuitive if the webapp --listen parameter accepted a port specifier too allowing configuration of the port.
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For my workflow, I thought I would contain all of git annexes dependencies inside a docker image since I'm quite comfortable with docker(and emerge on gentoo took a long time and finally failed). With an unconfigurable dynamic port though, it makes running the webapp subcommand in docker not really viable since I don't want to use docker run's port range mapping feature which will lock all those ports.
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### What steps will reproduce the problem?
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Dockerfile:
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ARG DEBIAN_TAG=buster-slim
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FROM debian:${DEBIAN_TAG}
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RUN set -ex \
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&& apt-get update \
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&& apt-get install -y \
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git \
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git-annex
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docker build -t git-annex:test .
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docker run --rm -it git-annex:test git annex webapp --listen 0.0.0.0:8888
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### What version of git-annex are you using? On what operating system?
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git-annex version: 7.20190129
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build flags: Assistant Webapp Pairing S3(multipartupload)(storageclasses) WebDAV Inotify DBus DesktopNotify TorrentParser MagicMime Feeds Testsuite
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dependency versions: aws-0.20 bloomfilter-2.0.1.0 cryptonite-0.25 DAV-1.3.3 feed-1.0.0.0 ghc-8.4.4 http-client-0.5.13.1 persistent-sqlite-2.8.2 torrent-10000.1.1 uuid-1.3.13 yesod-1.6.0
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### Please provide any additional information below.
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[[!format sh """
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# If you can, paste a complete transcript of the problem occurring here.
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# If the problem is with the git-annex assistant, paste in .git/annex/daemon.log
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# End of transcript or log.
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"""]]
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### Have you had any luck using git-annex before? (Sometimes we get tired of reading bug reports all day and a lil' positive end note does wonders)
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git annex seems awesome with the little bit of testing I've done. It seems like the perfect tool for what I want to accomplish. Thanks!
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### Please describe the problem.
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Original report: https://github.com/datalad/datalad/issues/3825
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[[!format sh """
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$> git annex addurl --json --json-error-messages s3://hcp-openaccess/HCP_1200/100206/.xdlm/100206_3T_Diffusion_unproc.json
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Configuration does not allow accessing s3://hcp-openaccess/HCP_1200/100206/.xdlm/100206_3T_Diffusion_unproc.json
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download failed: Configuration does not allow accessing s3://hcp-openaccess/HCP_1200/100206/.xdlm/100206_3T_Diffusion_unproc.json
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{"command":"addurl","success":false,"error-messages":[],"file":null}
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git-annex: addurl: 1 failed
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$> git annex version | head
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git-annex version: 7.20191009-1~ndall+1
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...
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"""]]
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the reason for the failure overall is that `datalad` external special remote is not enabled. So the error message might also be considered misleading -- it is not about "allowing" but rather being "not supported" since AFAIK git-annex doesn't support s3:// urls (see [an existing issue](https://git-annex.branchable.com/todo/Natively_support_s3__58____47____47___urls___40__for_addurl__44___get__44___etc__41__/))
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If user convenience was something to strive for here, it should technically be possible for git annex to "sense" all available external special remotes and inquire them (without enabling) either they would support a given url, and then report to the user a more informative error message ("URL ... is not supported by git-annex. You can initialize one of the available external special remotes which support that url: datalad, somebodies-s3, ...". It could even check if the special remote is configured but not enabled and then replace "initialize" with "enable" in the message above).
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[[!meta author=yoh]]
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[[!tag projects/datalad]]
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@ -116,4 +116,4 @@ Shouldn't that URL be recorded in remote.log? (similarly to `type=git` remotes)
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[[!meta author=yoh]]
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[[!tag projects/dandi]]
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> [[done]; see my comment --[[Joey]]
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> [[done]]; see my comment --[[Joey]]
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